AMBER Archive (2006)

Subject: AMBER: Modify charges to increase/decrease hydrogen bond interaction

From: Mingfeng Yang (
Date: Mon Aug 14 2006 - 13:25:19 CDT


I know that a specific residue (Ser) can form multiple hydrogen bonds with
other residues in the same protein, which should help to form and stabilize
a turn structure. Now I want to investigate the importance this hydrogen
bond. The charge of oxygen atom in the hydroxyl group of Ser is -0.6546, and
0.4275 of hydrogen thereof. I plan to increase the charge of oxygen atom
gradually to zero, and decrease the charge of hydrogen atom with the same
quantity at the same time, and observe the hydrogen bond network of this Ser
residue. This modification will be applied to the interaction between Ser
and all other residues, but when the intra-residue interactions are
evaluated, the charges remain the same as what amber force field gives. Does
my research design make sense?

Thanks for any input!


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